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Probing Changes in the Conformation of tRNAPhe: An Integrated Biochemistry Laboratory Course

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Sarah R. Kirk , Todd P. Silverstein , Karen L. McFarlane Holman and Buck L. H. Taylor

Department of Chemistry, Willamette University, Salem, OR 97301

J. Chem. Educ., 2008, 85 (5), p 666

DOI: 10.1021/ed085p666

Publication Date (Web): May 1, 2008

Abstract

We have designed a new guided-inquiry laboratory for an advanced biochemistry course. This integrated laboratory focuses on the biomolecule tRNA^Phe and combines elements of bioorganic and bioinorganic chemistry with biochemistry. Throughout the semester students work together to study tRNA^Phe structure and ligand binding by (i) assaying metal-catalyzed hydrolysis using gel electrophoresis; (ii) probing thermal denaturation with UV–vis spectrophotometry; and (iii) characterizing ligand associated changes in conformation via fluorescence spectroscopy. Students begin the course with a common laboratory experience and then diverge into parallel projects, ending with a novel self-designed project. In their final report, students interpret experimental results from the entire class and draw conclusions regarding the effects of various ligands on the structure of tRNA^Phe.

Keywords (Audience):

Upper-Division Undergraduate

Keywords (Domain):

Biochemistry

Keywords (Pedagogy):

Collaborative / Cooperative Learning

Keywords (Subject):

Bioinorganic Chemistry

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This article has been cited by 4 ACS Journal articles (4 most recent appear below).

An Undergraduate Investigation into the 10-23 DNA Enzyme That Cleaves RNA: DNA Can Cut It in the Biochemistry Laboratory
Amber Flynn-Charlebois, Jamie Burns, Stephanie Chapelliquen, and Holly Sanmartino
Journal of Chemical Education2011 88 (2), 226-228
- An Undergraduate Investigation into the 10-23 DNA Enzyme That Cleaves RNA: DNA Can Cut It in the Biochemistry Laboratory
  Amber Flynn-Charlebois, Jamie Burns, Stephanie Chapelliquen, and Holly Sanmartino
  Journal of Chemical Education2011 88 (2), 226-228
  A low-cost biochemistry experiment is described that demonstrates current techniques in the use of catalytic DNA molecules and introduces a nonradioactive, nonfluorescent, inexpensive, fast, and safe method for monitoring these nucleic acid reactions. The ...
  Abstract | Full Text HTML | Hi-Res PDF | PDF w/ Links
UV Thermal Melting Curves of tRNAPhe in the Presence of Ligands
Sarah R. Kirk , Todd P. Silverstein and Karen L. McFarlane Holman
Journal of Chemical Education2008 85 (5), 674
- UV Thermal Melting Curves of tRNAPhe in the Presence of Ligands
  Sarah R. Kirk , Todd P. Silverstein and Karen L. McFarlane Holman
  Journal of Chemical Education2008 85 (5), 674
  This laboratory project is one component of a semester-long advanced biochemistry laboratory course that uses several complementary techniques to study tRNAPhe conformational chvanges induced by ligand binding. In this article we describe a set of ...
  Abstract | Hi-Res PDF | PDF w/ Links
Metal-Catalyzed Cleavage of tRNAPhe
Sarah R. Kirk , Todd P. Silverstein and Karen L. McFarlane Holman
Journal of Chemical Education2008 85 (5), 676
- Metal-Catalyzed Cleavage of tRNAPhe
  Sarah R. Kirk , Todd P. Silverstein and Karen L. McFarlane Holman
  Journal of Chemical Education2008 85 (5), 676
  This laboratory project is one component of a semester-long advanced biochemistry laboratory course that uses several complementary techniques to study tRNAPhe conformational changes induced by ligand binding. In this article we describe a set of ...
  Abstract | Hi-Res PDF | PDF w/ Links
Fluorescence Spectroscopy of tRNAPhe Y Base in the Presence of Mg2+ and Small Molecule Ligands
Sarah R. Kirk , Todd P. Silverstein and Karen L. McFarlane Holman
Journal of Chemical Education2008 85 (5), 678
- Fluorescence Spectroscopy of tRNAPhe Y Base in the Presence of Mg2+ and Small Molecule Ligands
  Sarah R. Kirk , Todd P. Silverstein and Karen L. McFarlane Holman
  Journal of Chemical Education2008 85 (5), 678
  This laboratory project is one component of a semester-long advanced biochemistry laboratory course that uses several complementary techniques to study tRNAPhe conformational changes induced by ligand binding. In this article we describe a set of ...
  Abstract | Hi-Res PDF | PDF w/ Links